Welcome to the Adsorber documentation!¶
Section author: Geoffrey Weal <geoffrey.weal@gmail.com>
Section author: Dr. Anna Garden <anna.garden@otago.ac.nz>
Group page: https://blogs.otago.ac.nz/annagarden/
What is Adsorber¶
Adsorber is a program designed to adsorb molecules in various way to the surface of a cluster or a surface. This program adsorbed molecules ontop of atoms, ontop of bridge sites, ontop of three-fold sites, and ontop of four fold sites.
A guide on how to use the Adsorber
program is given in Guide To Using Adsorber.
This program is definitely a “work in progress”. I have made it as easy to use as possible, but there are always oversights to program development and some parts of it may not be as easy to use as it could be. If you have any issues with the program or you think there would be better/easier ways to use and implement things in Adsorber
, feel free to email Geoffrey about these (geoffrey.weal@gmail.com). Feedback is very much welcome!
Installation¶
It is recommended to read the installation page before using the Adsorber program. See Installation: Setting Up Adsorber and Pre-Requisites Packages for more information. Note that you can install Adsorber through pip3
and conda
.
As well as installing Adsorber, the Atomic Simulation Environment (ASE) GUI and Jmol programs are also used to visualise your system with adsorbed atoms and molecules upon it. Installation and how to use the ASE GUI and Jmol can be found in External Programs that will be useful to install for using Adsorber.
Guide To Using Adsorber¶
After you have installed Adsorber and all other helpful programs, see Guide To Using Adsorber to learn about the process of using Adsorber to obtain models of your system with various adsorbates for further optimisation with VASP.
Table of Contents¶
- Installation: Setting Up Adsorber and Pre-Requisites Packages
- External Programs that will be useful to install for using
Adsorber
- Guide To Using Adsorber
- Prelude 1: Run_Adsorber.py - Running Adsorber
- Prelude 2: How to obtain some of the settings for the
Run_Adsorber.py
script - Part A: How to optimise your system initially
- Part B: Adsorbing Adsorbates to your System
- How to Choose Which
xyz
Files to Optimise in VASP - Selecting binding sites using the
Label
command in Jmol - Advice on how I Choose
xyz
Files for VASP Optimise withAdsorber
- How to automate the copying of these
xyz
files: Usingcopy_files_from_folder_B_to_C.py
- What To Do Once You Have Placed Selected
xyz
Files IntoPart_C_Selected_Systems_with_Adsorbed_Species_to_Convert_into_VASP_files
- How to Choose Which
- Part C.1: Preparing Selected Adsorbed Systems For VASP Optimisation
- What will
Run_Adsorber.py
: Part C do? - I accidentally gave wrong settings in the
INCAR
orsubmit.sl
files, or something about myKPOINTS
orPOTCAR
. What should I do? - I want to add more new places that adsorbates can bind to on the surface of the cluster/surface model in Part B, what do I do here?
- How to submit VASP jobs to Slurm: The
Run_Adsorber_submitSL_slurm.py
program - What to do if some jobs need to be resubmit for some reason
- What will
- Part C.2: What To Do If Some Jobs Have Not Finished/Converged
- Part D: Gathering Information from VASP Calculations
- Index
- Python Module Index